{"id":9478,"date":"2022-09-07T15:42:00","date_gmt":"2022-09-07T19:42:00","guid":{"rendered":"https:\/\/www.furman.edu\/news\/2021\/07\/30\/fungi-focus-of-students-simulation\/"},"modified":"2025-07-30T17:55:34","modified_gmt":"2025-07-30T21:55:34","slug":"fungi-focus-of-students-simulation","status":"publish","type":"post","link":"https:\/\/www.furman.edu\/news\/fungi-focus-of-students-simulation\/","title":{"rendered":"Fungi focus of student’s simulation"},"content":{"rendered":"

Just like bacteria, fungi can develop resistance to drugs used to treat infections, a \u201cgrowing threat\u201d across the country, according to the Centers for Disease Control and Prevention<\/a>. With only three classes of anti-fungal medications, the need to find new ways to combat fungal infections is increasingly important.<\/p>\n

\"A<\/a>

A computer model of Pho85 by Mason Dudley ’23.<\/p><\/div>\n

One Furman University student is contributing to the understanding of drug-resistant fungi. Mason Dudley \u201923 is working to create a computer model of a protein that causes drug resistance in the fungus Candida glabrata<\/a>. He\u2019s working with chemistry professor George Shields, chemistry assistant professor Meghan Breen and Karl Kirschner, who is on faculty at Bonn Rhein-Sieg University of Applied Sciences in Germany.<\/p>\n

We asked Dudley about his research. His answers are below.<\/p>\n

What\u2019s your research about?<\/strong><\/p>\n

We are working creating a model of a protein, Pho85, that is responsible for drug resistance in C. glabrata, a common fungal infection, and we are also working on simulating the activation of it as well. A cyclin is a protein that has roles in cell division, in this case when our protein Pho85 is paired with a cyclin it has additional rolls in the cell such as the phosphorous pathway, which is why we are interested in this protein.<\/p>\n

My research is focused on computationally investigating a cyclin dependent kinase (CDK) that, when phosphorylated, is responsible for activation of PDR1, a transcription factor that causes azole drug resistance in C. glabrata. So far, I modeled the protein as well as its major cyclin, Pho80, and have begun to run molecular dynamics to understand how this protein acts within the body.<\/p>\n

Why does this research interest you?<\/strong><\/p>\n

This research is interesting as azoles are becoming a less effective treatment for fungal infections, especially with C. glabrata, leading to a possible rise in super fungi.<\/p>\n

Where has your research taken you so far?<\/strong><\/p>\n

We have generated a visual that shows the\u00a0flexibility of the cdk itself, as well shows the motion of the ATP\u00a0binding in Pho85. I am currently working on using a mix of quantum mechanics and molecular mechanics to\u00a0simulate the hydrolysis of ATP within this protein, where a single phosphate will\u00a0transfer to the protein simulating the\u00a0theoretical mechanism of activation leading to activation of PDR1. I\u00a0have a video that shows the movement of protein throughout the molecular\u00a0dynamics simulations if you want me to send it to you.<\/p>\n

Has anything surprised you?<\/strong><\/p>\n

Not much has surprised me other than how fast and how much data\u00a0I can generate. One 100 nano-second simulation of this\u00a0protein generates a 100-gigabyte trajectory file that helps us to visualize the movement. So far, I have generated over 10 terabytes of data for this protein, having made 100 replicas, and have plans to generate a total of over 50TB of data when\u00a0I begin to run molecular dynamics on its cyclin Pho80.<\/p>\n

What does being able to do research mean to you?<\/strong><\/p>\n

Research to me means being to\u00a0learn many different skills and work with a diverse group of people.<\/p>\n","protected":false},"excerpt":{"rendered":"

Just like bacteria, fungi can develop resistance to drugs used to treat infections, a \u201cgrowing threat\u201d across the country, according to the Centers for Disease Control and Prevention. With only […]<\/p>\n","protected":false},"author":389,"featured_media":9479,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"footnotes":""},"categories":[15,26,53,13,55],"tags":[],"class_list":["post-9478","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-academic-department-page","category-administrative","category-chemistry","category-top-four-news-4th-story","category-undergraduate-research"],"acf":[],"_links":{"self":[{"href":"https:\/\/www.furman.edu\/news\/wp-json\/wp\/v2\/posts\/9478","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.furman.edu\/news\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.furman.edu\/news\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.furman.edu\/news\/wp-json\/wp\/v2\/users\/389"}],"replies":[{"embeddable":true,"href":"https:\/\/www.furman.edu\/news\/wp-json\/wp\/v2\/comments?post=9478"}],"version-history":[{"count":1,"href":"https:\/\/www.furman.edu\/news\/wp-json\/wp\/v2\/posts\/9478\/revisions"}],"predecessor-version":[{"id":38856,"href":"https:\/\/www.furman.edu\/news\/wp-json\/wp\/v2\/posts\/9478\/revisions\/38856"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.furman.edu\/news\/wp-json\/wp\/v2\/media\/9479"}],"wp:attachment":[{"href":"https:\/\/www.furman.edu\/news\/wp-json\/wp\/v2\/media?parent=9478"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.furman.edu\/news\/wp-json\/wp\/v2\/categories?post=9478"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.furman.edu\/news\/wp-json\/wp\/v2\/tags?post=9478"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}